Closed:Velvetg error coverage=0

Question

[blanca]

Hello!

I am trying to assemble 454 metagenomes with MetaVelvet. I will try other assemblers later on (suggestions accepted), but right now I am stuck with this.

I follow the "getting started" section on meta-velvet webpage (http://metavelvet.dna.bio.keio.ac.jp/MV.html#download), adapted to 454 sequences, that is-to my knowledge-:

velveth out_dir/ [k-mer] -long metagenome.fasta

This creates Log, Roadmap, Sequences. The problem is velvetg step:

velvetg out_dir/ -exp_cov auto
[0.000000] Reading roadmap file out_dir//Roadmaps
[1.530237] 1289893 roadmaps read
[1.531154] Creating insertion markers
[1.582196] Ordering insertion markers
[1.621266] Counting preNodes
[1.651521] 310083 preNodes counted, creating them now
[22.031771] Sequence 1000000 / 1289893
[27.818683] Adjusting marker info...
[27.841544] Connecting preNodes
[27.864501] Connecting 1000000 / 1289893
[27.921674] Cleaning up memory
[27.922153] Done creating preGraph
[27.922159] Concatenation...
[28.275135] Renumbering preNodes
[28.275153] Initial preNode count 310083
[28.297748] Destroyed 174841 preNodes
[28.297769] Concatenation over!
[28.297772] Clipping short tips off preGraph
[28.358773] Concatenation...
[28.396268] Renumbering preNodes
[28.396278] Initial preNode count 135242
[28.397166] Destroyed 128595 preNodes
[28.397173] Concatenation over!
[28.397175] 120187 tips cut off
[28.397177] 6647 nodes left
[28.406319] Writing into pregraph file out_dir//PreGraph...
[28.772199] Reading read set file out_dir//Sequences;
[29.811531] 1289893 sequences found
[33.506199] Done
[36.183420] Reading pre-graph file out_dir//PreGraph
[36.183488] Graph has 6647 nodes and 1289893 sequences
[36.362304] Scanning pre-graph file out_dir//PreGraph for k-mers
[36.545621] 3248177 kmers found
[37.078556] Sorting kmer occurence table ... 
[39.563009] Sorting done.
[39.563034] Computing acceleration table... 
[39.664495] Computing offsets... 
[39.740276] Ghost Threading through reads 0 / 1289893
[39.744659] Ghost Threading through reads 1000000 / 1289893
[39.763480]  === Ghost-Threaded in 0.045164 s
[39.774349] Threading through reads 0 / 1289893
[43.101249] Threading through reads 1000000 / 1289893
[55.701484]  === Threaded in 15.937996 s
[55.720859] Correcting graph with cutoff 0.200000
[55.721779] Determining eligible starting points
[55.739227] Done listing starting nodes
[55.739234] Initializing todo lists
[55.740025] Done with initilization
[55.740030] Activating arc lookup table
[55.740807] Done activating arc lookup table
[55.758133] Concatenation...
[55.758533] Renumbering nodes
[55.758538] Initial node count 6647
[55.758551] Removed 0 null nodes
[55.758557] Concatenation over!
[55.758560] Clipping short tips off graph, drastic
[55.768814] Concatenation...
[55.789225] Renumbering nodes
[55.789233] Initial node count 6647
[55.789398] Removed 4445 null nodes
[55.789403] Concatenation over!
[55.789406] 2202 nodes left
[55.789473] Writing into graph file out_dir//Graph2...
[56.192893] Measuring median coverage depth...
[56.193968] Median coverage depth = 0.000000
[56.194007] Removing contigs with coverage < 0.000000...
[56.194325] Concatenation...
[56.194462] Renumbering nodes
[56.194465] Initial node count 2202
[56.194470] Removed 0 null nodes
[56.194473] Concatenation over!
[56.194610] Concatenation...
[56.194690] Renumbering nodes
[56.194693] Initial node count 2202
[56.194697] Removed 0 null nodes
[56.194699] Concatenation over!
[56.194704] Clipping short tips off graph, drastic
[56.194840] Concatenation...
[56.194920] Renumbering nodes
[56.194923] Initial node count 2202
[56.194927] Removed 0 null nodes
[56.194929] Concatenation over!
[56.194931] 2202 nodes left
[56.194933] WARNING: NO EXPECTED COVERAGE PROVIDED
[56.194938] Velvet will be unable to resolve any repeats
[56.194940] See manual for instructions on how to set the expected coverage parameter
[56.194942] Concatenation...
[56.195019] Renumbering nodes
[56.195021] Initial node count 2202
[56.195026] Removed 0 null nodes
[56.195028] Concatenation over!
[56.195030] Removing reference contigs with coverage < 0.000000...
[56.199145] Concatenation...
[56.199232] Renumbering nodes
[56.199235] Initial node count 2202
[56.199240] Removed 0 null nodes
[56.199241] Concatenation over!
[56.206252] Writing contigs into out_dir//contigs.fa...
[56.508126] Writing into stats file out_dir//stats.txt...
[56.601783] Writing into graph file out_dir//LastGraph...
[56.976779] Estimated Coverage = 0.000000
[56.976796] Estimated Coverage cutoff = 0.000000
Final graph has 2202 nodes and n50 of 1367, max 13331, total 2520678, using 46744/1289893 reads

I have tried using: `velvetg /home/blanca/out_dir2/ -exp_cov auto -cov_cutoff auto`` but I get the same error.

Otherwise, it creates contigs.fa, Graph2, LastGraph, PreGraph, stats.txt

The representation of stats.txt with R (weighted.hist(data$short1_cov, data$lgth, breaks=seq(0, 200, by=1))), gives this graph with a bar in 0 coverage.

Does someone have any suggestion?

Thank you!

Note: without the option -long in velveth command, it runs -apparently- perfectly. This error doesn't show, but as it is a 454 dataset, I'd rather use the -long option, right?